Multiple sequence alignment - TraesCS3D01G190500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G190500 chr3D 100.000 4390 0 0 1 4390 179082578 179086967 0.000000e+00 8107.0
1 TraesCS3D01G190500 chr3D 88.646 229 26 0 2 230 376986387 376986615 3.340000e-71 279.0
2 TraesCS3D01G190500 chr3D 88.889 225 24 1 6 230 174476558 174476781 4.320000e-70 276.0
3 TraesCS3D01G190500 chr3D 83.550 231 35 3 1 230 260226253 260226025 3.440000e-51 213.0
4 TraesCS3D01G190500 chr3D 100.000 81 0 0 976 1056 196981129 196981049 2.740000e-32 150.0
5 TraesCS3D01G190500 chr3D 91.743 109 8 1 3588 3696 355968201 355968094 2.740000e-32 150.0
6 TraesCS3D01G190500 chr3D 96.610 59 2 0 811 869 196981181 196981123 1.000000e-16 99.0
7 TraesCS3D01G190500 chr3B 94.074 1755 69 13 1855 3593 257211311 257213046 0.000000e+00 2632.0
8 TraesCS3D01G190500 chr3B 93.099 1449 58 20 299 1728 257209607 257211032 0.000000e+00 2084.0
9 TraesCS3D01G190500 chr3B 92.638 489 23 6 3873 4349 104699617 104700104 0.000000e+00 691.0
10 TraesCS3D01G190500 chr3B 87.826 230 28 0 1 230 698662603 698662374 2.010000e-68 270.0
11 TraesCS3D01G190500 chr3B 87.391 230 29 0 1 230 698725769 698725540 9.360000e-67 265.0
12 TraesCS3D01G190500 chr3B 92.157 153 11 1 1720 1872 257211120 257211271 9.560000e-52 215.0
13 TraesCS3D01G190500 chr3B 85.024 207 29 2 1858 2063 48102175 48101970 4.450000e-50 209.0
14 TraesCS3D01G190500 chr3B 85.024 207 29 2 1858 2063 706219749 706219544 4.450000e-50 209.0
15 TraesCS3D01G190500 chr3B 97.727 44 0 1 3794 3836 257213099 257213142 1.690000e-09 75.0
16 TraesCS3D01G190500 chr3A 94.238 1562 63 13 1855 3398 221668780 221670332 0.000000e+00 2361.0
17 TraesCS3D01G190500 chr3A 96.768 1114 29 3 765 1872 221667628 221668740 0.000000e+00 1851.0
18 TraesCS3D01G190500 chr3A 91.469 715 40 12 1 708 221666606 221667306 0.000000e+00 963.0
19 TraesCS3D01G190500 chr3A 84.375 416 49 10 1162 1570 599780903 599780497 1.140000e-105 394.0
20 TraesCS3D01G190500 chr3A 95.092 163 8 0 3431 3593 221670329 221670491 1.570000e-64 257.0
21 TraesCS3D01G190500 chr3A 86.782 174 12 7 803 975 599781061 599780898 2.700000e-42 183.0
22 TraesCS3D01G190500 chr2D 87.686 1007 82 16 803 1800 469922045 469921072 0.000000e+00 1134.0
23 TraesCS3D01G190500 chr2D 88.927 578 33 8 3838 4390 540175885 540175314 0.000000e+00 684.0
24 TraesCS3D01G190500 chr2D 85.879 347 34 6 1952 2287 469920895 469920553 5.400000e-94 355.0
25 TraesCS3D01G190500 chr2D 85.714 203 27 2 1862 2063 68868782 68868581 3.440000e-51 213.0
26 TraesCS3D01G190500 chr2D 93.333 105 7 0 3592 3696 316334112 316334008 5.880000e-34 156.0
27 TraesCS3D01G190500 chr7B 87.591 959 77 18 803 1753 699039595 699040519 0.000000e+00 1074.0
28 TraesCS3D01G190500 chr7B 89.503 543 29 7 3873 4390 179633739 179634278 0.000000e+00 662.0
29 TraesCS3D01G190500 chr7B 85.552 353 37 5 1943 2284 699040571 699040920 1.500000e-94 357.0
30 TraesCS3D01G190500 chr7B 84.136 353 35 9 1943 2284 693507162 693507504 5.480000e-84 322.0
31 TraesCS3D01G190500 chr7D 90.240 584 26 7 3834 4390 46096965 46097544 0.000000e+00 734.0
32 TraesCS3D01G190500 chr7D 88.448 580 34 9 3838 4390 535313608 535314181 0.000000e+00 669.0
33 TraesCS3D01G190500 chr7D 80.180 222 39 4 2 221 191039361 191039143 1.260000e-35 161.0
34 TraesCS3D01G190500 chr6D 89.100 578 34 6 3838 4390 263995908 263996481 0.000000e+00 691.0
35 TraesCS3D01G190500 chr6D 90.074 544 26 4 3873 4390 59749218 59749759 0.000000e+00 680.0
36 TraesCS3D01G190500 chr6D 91.820 489 26 6 3873 4349 173912564 173912078 0.000000e+00 669.0
37 TraesCS3D01G190500 chr6D 86.512 215 29 0 7 221 355815237 355815023 2.040000e-58 237.0
38 TraesCS3D01G190500 chr6D 93.396 106 7 0 3591 3696 72350886 72350991 1.630000e-34 158.0
39 TraesCS3D01G190500 chr6D 92.453 106 8 0 3591 3696 461504796 461504691 7.600000e-33 152.0
40 TraesCS3D01G190500 chr6B 92.008 488 21 4 3873 4347 623359279 623359761 0.000000e+00 669.0
41 TraesCS3D01G190500 chr4B 92.421 475 23 2 3873 4335 649148391 649148864 0.000000e+00 665.0
42 TraesCS3D01G190500 chr4B 88.571 210 21 2 21 230 534414723 534414517 7.290000e-63 252.0
43 TraesCS3D01G190500 chr4B 80.000 130 21 5 65 192 231829067 231828941 1.680000e-14 91.6
44 TraesCS3D01G190500 chrUn 87.971 557 26 9 3873 4390 311996429 311996983 1.730000e-173 619.0
45 TraesCS3D01G190500 chrUn 83.275 568 29 16 3873 4389 348455168 348455720 3.090000e-126 462.0
46 TraesCS3D01G190500 chrUn 83.245 567 29 17 3873 4389 32019630 32020180 1.110000e-125 460.0
47 TraesCS3D01G190500 chrUn 83.245 567 29 17 3873 4389 320531864 320531314 1.110000e-125 460.0
48 TraesCS3D01G190500 chrUn 81.996 511 26 16 3930 4389 31967336 31967831 1.490000e-99 374.0
49 TraesCS3D01G190500 chr7A 95.156 289 14 0 3876 4164 538296943 538296655 1.440000e-124 457.0
50 TraesCS3D01G190500 chr7A 84.354 147 15 7 3584 3724 472631314 472631458 2.130000e-28 137.0
51 TraesCS3D01G190500 chr5B 84.906 265 31 6 1610 1872 684374374 684374117 4.360000e-65 259.0
52 TraesCS3D01G190500 chr5B 84.541 207 30 2 1858 2063 143730709 143730914 2.070000e-48 204.0
53 TraesCS3D01G190500 chr5B 84.615 208 29 3 1858 2063 684374074 684373868 2.070000e-48 204.0
54 TraesCS3D01G190500 chr5B 84.577 201 31 0 1 201 66749502 66749302 2.680000e-47 200.0
55 TraesCS3D01G190500 chr5B 93.333 105 7 0 3592 3696 682955534 682955430 5.880000e-34 156.0
56 TraesCS3D01G190500 chr1B 85.149 202 28 2 1863 2063 439527512 439527312 5.760000e-49 206.0
57 TraesCS3D01G190500 chr4D 81.991 211 37 1 1 211 279896783 279896574 1.250000e-40 178.0
58 TraesCS3D01G190500 chr4D 92.593 108 8 0 3592 3699 259381898 259381791 5.880000e-34 156.0
59 TraesCS3D01G190500 chr1A 81.106 217 37 2 1 214 165134204 165134419 2.100000e-38 171.0
60 TraesCS3D01G190500 chr5D 93.333 105 7 0 3592 3696 11004574 11004470 5.880000e-34 156.0
61 TraesCS3D01G190500 chr1D 91.743 109 8 1 3588 3696 270960221 270960328 2.740000e-32 150.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G190500 chr3D 179082578 179086967 4389 False 8107.0 8107 100.00000 1 4390 1 chr3D.!!$F2 4389
1 TraesCS3D01G190500 chr3B 257209607 257213142 3535 False 1251.5 2632 94.26425 299 3836 4 chr3B.!!$F2 3537
2 TraesCS3D01G190500 chr3A 221666606 221670491 3885 False 1358.0 2361 94.39175 1 3593 4 chr3A.!!$F1 3592
3 TraesCS3D01G190500 chr3A 599780497 599781061 564 True 288.5 394 85.57850 803 1570 2 chr3A.!!$R1 767
4 TraesCS3D01G190500 chr2D 469920553 469922045 1492 True 744.5 1134 86.78250 803 2287 2 chr2D.!!$R4 1484
5 TraesCS3D01G190500 chr2D 540175314 540175885 571 True 684.0 684 88.92700 3838 4390 1 chr2D.!!$R3 552
6 TraesCS3D01G190500 chr7B 699039595 699040920 1325 False 715.5 1074 86.57150 803 2284 2 chr7B.!!$F3 1481
7 TraesCS3D01G190500 chr7B 179633739 179634278 539 False 662.0 662 89.50300 3873 4390 1 chr7B.!!$F1 517
8 TraesCS3D01G190500 chr7D 46096965 46097544 579 False 734.0 734 90.24000 3834 4390 1 chr7D.!!$F1 556
9 TraesCS3D01G190500 chr7D 535313608 535314181 573 False 669.0 669 88.44800 3838 4390 1 chr7D.!!$F2 552
10 TraesCS3D01G190500 chr6D 263995908 263996481 573 False 691.0 691 89.10000 3838 4390 1 chr6D.!!$F3 552
11 TraesCS3D01G190500 chr6D 59749218 59749759 541 False 680.0 680 90.07400 3873 4390 1 chr6D.!!$F1 517
12 TraesCS3D01G190500 chrUn 311996429 311996983 554 False 619.0 619 87.97100 3873 4390 1 chrUn.!!$F3 517
13 TraesCS3D01G190500 chrUn 348455168 348455720 552 False 462.0 462 83.27500 3873 4389 1 chrUn.!!$F4 516
14 TraesCS3D01G190500 chrUn 32019630 32020180 550 False 460.0 460 83.24500 3873 4389 1 chrUn.!!$F2 516
15 TraesCS3D01G190500 chrUn 320531314 320531864 550 True 460.0 460 83.24500 3873 4389 1 chrUn.!!$R1 516
16 TraesCS3D01G190500 chr5B 684373868 684374374 506 True 231.5 259 84.76050 1610 2063 2 chr5B.!!$R3 453

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
467 470 0.400213 ACCAGCGTTGATTTCAGGGA 59.600 50.0 0.0 0.0 0.0 4.20 F
1945 2406 0.883833 GGTCATTCTTGTGCTGGTGG 59.116 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2427 2900 0.038310 CTCCCCCACTTCCCAAACTC 59.962 60.0 0.0 0.0 0.00 3.01 R
3789 4276 0.252197 GGACCAGACCATACGGCTTT 59.748 55.0 0.0 0.0 34.57 3.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.238497 CACACGTGGTCCTCCCCA 61.238 66.667 21.57 0.00 0.00 4.96
102 103 2.801631 CCGAGGAGACCCATGCCTC 61.802 68.421 6.31 6.31 43.73 4.70
256 257 3.068590 GTCATAAATTGGTGGGCCATCAG 59.931 47.826 20.57 7.38 45.56 2.90
269 270 1.335324 GCCATCAGTGTGTTTGACAGC 60.335 52.381 0.00 0.00 34.28 4.40
273 274 4.500205 CCATCAGTGTGTTTGACAGCAAAT 60.500 41.667 0.00 0.00 45.01 2.32
288 289 8.887036 TGACAGCAAATACGAGAATGTTATAT 57.113 30.769 0.00 0.00 0.00 0.86
348 349 1.473677 CATGGAAGGCAGCGATTTCAA 59.526 47.619 0.00 0.00 0.00 2.69
381 382 4.157289 AGCTGGCTATCACAACTGAATTTG 59.843 41.667 0.00 0.00 0.00 2.32
382 383 4.418392 CTGGCTATCACAACTGAATTTGC 58.582 43.478 0.00 0.00 0.00 3.68
386 387 2.798976 TCACAACTGAATTTGCAGGC 57.201 45.000 0.00 0.00 40.20 4.85
406 408 4.535526 GCCTTCTTTTCATGGCCTAAAA 57.464 40.909 3.32 7.62 39.49 1.52
459 462 4.805219 GGTTAAATCAAACCAGCGTTGAT 58.195 39.130 0.00 0.00 46.85 2.57
467 470 0.400213 ACCAGCGTTGATTTCAGGGA 59.600 50.000 0.00 0.00 0.00 4.20
470 476 2.295909 CCAGCGTTGATTTCAGGGAAAA 59.704 45.455 0.00 0.00 35.11 2.29
693 709 1.134788 CCCTCGCAAAGTAGTGGTAGG 60.135 57.143 0.00 0.00 0.00 3.18
890 1171 1.590259 GCGCTCTTGATCCCTCGTC 60.590 63.158 0.00 0.00 0.00 4.20
1102 1384 1.337071 TCGAGATCGACCAAGGTATGC 59.663 52.381 0.00 0.00 44.22 3.14
1286 1568 5.864628 AGCTTACTTTCAAGATCGGTTTC 57.135 39.130 0.00 0.00 0.00 2.78
1775 2163 8.959548 TGACTGTTTCATCAATTAGCATATTGT 58.040 29.630 9.69 0.00 36.95 2.71
1859 2248 5.587844 GTCAATGTCCAGAAATAGCATCTGT 59.412 40.000 3.18 0.00 42.19 3.41
1860 2249 5.587443 TCAATGTCCAGAAATAGCATCTGTG 59.413 40.000 3.18 0.00 42.19 3.66
1861 2250 4.824479 TGTCCAGAAATAGCATCTGTGA 57.176 40.909 3.18 0.00 42.19 3.58
1911 2366 8.631480 TCTATCTAAACCTTTGTCCTTTTTCC 57.369 34.615 0.00 0.00 0.00 3.13
1923 2378 2.091333 TCCTTTTTCCCCTTTGCTGTCT 60.091 45.455 0.00 0.00 0.00 3.41
1945 2406 0.883833 GGTCATTCTTGTGCTGGTGG 59.116 55.000 0.00 0.00 0.00 4.61
1948 2409 1.142667 TCATTCTTGTGCTGGTGGACA 59.857 47.619 0.00 0.00 42.73 4.02
2020 2482 7.628366 GCATGTATAAGGCACACATAACAGTTT 60.628 37.037 0.00 0.00 31.81 2.66
2029 2491 5.868801 GCACACATAACAGTTTAATGGCAAT 59.131 36.000 0.00 0.00 0.00 3.56
2033 2495 8.987890 ACACATAACAGTTTAATGGCAATTTTC 58.012 29.630 0.00 0.00 0.00 2.29
2315 2788 7.864882 AGGTTTCTAGTTCTACAAGTTTACGAC 59.135 37.037 0.00 0.00 0.00 4.34
2320 2793 8.408601 TCTAGTTCTACAAGTTTACGACAAGTT 58.591 33.333 0.00 0.00 0.00 2.66
2324 2797 6.331845 TCTACAAGTTTACGACAAGTTCACA 58.668 36.000 0.00 0.00 0.00 3.58
2405 2878 2.427095 CCAAGTAGCCTAATTTGGTGGC 59.573 50.000 7.77 5.71 46.42 5.01
2426 2899 2.323599 CTCTGGCCCACTATCATGAGA 58.676 52.381 0.00 0.00 0.00 3.27
2427 2900 2.299582 CTCTGGCCCACTATCATGAGAG 59.700 54.545 15.75 15.75 0.00 3.20
2428 2901 2.091111 TCTGGCCCACTATCATGAGAGA 60.091 50.000 23.69 0.00 0.00 3.10
2429 2902 2.299582 CTGGCCCACTATCATGAGAGAG 59.700 54.545 23.69 15.50 39.02 3.20
2448 2921 1.069775 GTTTGGGAAGTGGGGGAGTA 58.930 55.000 0.00 0.00 0.00 2.59
2467 2940 4.484912 AGTAAAGTTGGTCTCCTGAGTCT 58.515 43.478 0.00 0.00 0.00 3.24
2506 2979 2.472695 AGTGCAGCAGGTTAAATCGA 57.527 45.000 0.00 0.00 0.00 3.59
2520 2993 5.120363 GGTTAAATCGAAGAAAGAAGAGCGT 59.880 40.000 0.00 0.00 43.58 5.07
2529 3002 0.605589 AAGAAGAGCGTGTGAGAGGG 59.394 55.000 0.00 0.00 0.00 4.30
2559 3045 4.593206 TCCCGGAGATTTATGTCAGCTATT 59.407 41.667 0.73 0.00 0.00 1.73
2571 3057 9.920133 TTTATGTCAGCTATTTATTTTTGTGCA 57.080 25.926 0.00 0.00 0.00 4.57
2620 3106 5.451908 CACTAAAAGTCGCATGAAACATGT 58.548 37.500 12.27 0.00 0.00 3.21
2717 3203 9.275398 ACTAACCGACTTATTGAAAACAATGTA 57.725 29.630 0.00 0.00 0.00 2.29
2770 3256 1.202348 CGTGTGACCTATGACTGCTGA 59.798 52.381 0.00 0.00 0.00 4.26
2803 3289 3.632189 GTTTGTCCTGCAGCAAGTAAAG 58.368 45.455 8.66 0.00 0.00 1.85
2994 3480 6.757947 GCTTTCCATTTGCATAGCTTTTATCA 59.242 34.615 0.00 0.00 0.00 2.15
3037 3523 2.436824 GCTTCGCCCCTCAGTTCC 60.437 66.667 0.00 0.00 0.00 3.62
3047 3533 1.308998 CCTCAGTTCCGTTTGCTTGT 58.691 50.000 0.00 0.00 0.00 3.16
3101 3587 0.036952 CTGGTCGCAGATGGTCTTGT 60.037 55.000 0.00 0.00 40.67 3.16
3125 3611 6.578919 GTGTGTAGCATTTCTTTTTACTCTGC 59.421 38.462 0.00 0.00 0.00 4.26
3177 3663 9.214953 CGTCATAATCTCTTGAAGTAATTTTGC 57.785 33.333 0.00 0.00 0.00 3.68
3221 3707 8.805175 TGAATCTTGTATGGTGATGAAATTGTT 58.195 29.630 0.00 0.00 0.00 2.83
3249 3736 7.550196 GTCTCGTTAACCCCATTTTCTTGTATA 59.450 37.037 0.00 0.00 0.00 1.47
3422 3909 6.465751 CCCCATCCATATCAAAGCTGTAGTAA 60.466 42.308 0.00 0.00 0.00 2.24
3535 4022 4.179926 TCAGCACTGTGTATCAGACTTC 57.820 45.455 9.86 0.00 46.27 3.01
3558 4045 5.066375 TCGTACCGTACTGCATGTAGTTATT 59.934 40.000 21.91 6.97 32.19 1.40
3593 4080 4.608445 GCACAACTTGTCGAACAGTGATAC 60.608 45.833 0.00 0.00 0.00 2.24
3595 4082 4.982916 ACAACTTGTCGAACAGTGATACTC 59.017 41.667 0.00 0.00 0.00 2.59
3596 4083 4.175787 ACTTGTCGAACAGTGATACTCC 57.824 45.455 0.00 0.00 0.00 3.85
3598 4085 2.803956 TGTCGAACAGTGATACTCCCT 58.196 47.619 0.00 0.00 0.00 4.20
3599 4086 2.753452 TGTCGAACAGTGATACTCCCTC 59.247 50.000 0.00 0.00 0.00 4.30
3600 4087 2.099427 GTCGAACAGTGATACTCCCTCC 59.901 54.545 0.00 0.00 0.00 4.30
3602 4089 2.695666 CGAACAGTGATACTCCCTCCAT 59.304 50.000 0.00 0.00 0.00 3.41
3603 4090 3.133003 CGAACAGTGATACTCCCTCCATT 59.867 47.826 0.00 0.00 0.00 3.16
3604 4091 4.698575 GAACAGTGATACTCCCTCCATTC 58.301 47.826 0.00 0.00 0.00 2.67
3605 4092 3.041946 ACAGTGATACTCCCTCCATTCC 58.958 50.000 0.00 0.00 0.00 3.01
3606 4093 3.310954 ACAGTGATACTCCCTCCATTCCT 60.311 47.826 0.00 0.00 0.00 3.36
3607 4094 4.078571 ACAGTGATACTCCCTCCATTCCTA 60.079 45.833 0.00 0.00 0.00 2.94
3608 4095 4.901849 CAGTGATACTCCCTCCATTCCTAA 59.098 45.833 0.00 0.00 0.00 2.69
3609 4096 5.366768 CAGTGATACTCCCTCCATTCCTAAA 59.633 44.000 0.00 0.00 0.00 1.85
3610 4097 6.043706 CAGTGATACTCCCTCCATTCCTAAAT 59.956 42.308 0.00 0.00 0.00 1.40
3611 4098 7.235606 CAGTGATACTCCCTCCATTCCTAAATA 59.764 40.741 0.00 0.00 0.00 1.40
3612 4099 7.964293 AGTGATACTCCCTCCATTCCTAAATAT 59.036 37.037 0.00 0.00 0.00 1.28
3613 4100 9.268282 GTGATACTCCCTCCATTCCTAAATATA 57.732 37.037 0.00 0.00 0.00 0.86
3617 4104 8.616799 ACTCCCTCCATTCCTAAATATATCTC 57.383 38.462 0.00 0.00 0.00 2.75
3618 4105 8.413821 ACTCCCTCCATTCCTAAATATATCTCT 58.586 37.037 0.00 0.00 0.00 3.10
3619 4106 9.278011 CTCCCTCCATTCCTAAATATATCTCTT 57.722 37.037 0.00 0.00 0.00 2.85
3620 4107 9.635284 TCCCTCCATTCCTAAATATATCTCTTT 57.365 33.333 0.00 0.00 0.00 2.52
3621 4108 9.898152 CCCTCCATTCCTAAATATATCTCTTTC 57.102 37.037 0.00 0.00 0.00 2.62
3639 4126 5.171476 TCTTTCTAGAGATTCCAACAAGCG 58.829 41.667 0.00 0.00 0.00 4.68
3640 4127 4.801330 TTCTAGAGATTCCAACAAGCGA 57.199 40.909 0.00 0.00 0.00 4.93
3641 4128 4.111375 TCTAGAGATTCCAACAAGCGAC 57.889 45.455 0.00 0.00 0.00 5.19
3642 4129 3.764434 TCTAGAGATTCCAACAAGCGACT 59.236 43.478 0.00 0.00 0.00 4.18
3643 4130 4.948004 TCTAGAGATTCCAACAAGCGACTA 59.052 41.667 0.00 0.00 0.00 2.59
3644 4131 3.851098 AGAGATTCCAACAAGCGACTAC 58.149 45.455 0.00 0.00 0.00 2.73
3645 4132 3.511934 AGAGATTCCAACAAGCGACTACT 59.488 43.478 0.00 0.00 0.00 2.57
3646 4133 4.021016 AGAGATTCCAACAAGCGACTACTT 60.021 41.667 0.00 0.00 0.00 2.24
3647 4134 5.185249 AGAGATTCCAACAAGCGACTACTTA 59.815 40.000 0.00 0.00 0.00 2.24
3648 4135 5.169295 AGATTCCAACAAGCGACTACTTAC 58.831 41.667 0.00 0.00 0.00 2.34
3649 4136 2.937591 TCCAACAAGCGACTACTTACG 58.062 47.619 0.00 0.00 0.00 3.18
3650 4137 1.990563 CCAACAAGCGACTACTTACGG 59.009 52.381 0.00 0.00 0.00 4.02
3651 4138 2.352030 CCAACAAGCGACTACTTACGGA 60.352 50.000 0.00 0.00 0.00 4.69
3652 4139 2.915463 CAACAAGCGACTACTTACGGAG 59.085 50.000 0.00 0.00 0.00 4.63
3653 4140 2.430465 ACAAGCGACTACTTACGGAGA 58.570 47.619 0.00 0.00 0.00 3.71
3654 4141 2.816087 ACAAGCGACTACTTACGGAGAA 59.184 45.455 0.00 0.00 0.00 2.87
3655 4142 3.254166 ACAAGCGACTACTTACGGAGAAA 59.746 43.478 0.00 0.00 0.00 2.52
3656 4143 4.232221 CAAGCGACTACTTACGGAGAAAA 58.768 43.478 0.00 0.00 0.00 2.29
3657 4144 4.510038 AGCGACTACTTACGGAGAAAAA 57.490 40.909 0.00 0.00 0.00 1.94
3658 4145 5.069501 AGCGACTACTTACGGAGAAAAAT 57.930 39.130 0.00 0.00 0.00 1.82
3659 4146 4.863131 AGCGACTACTTACGGAGAAAAATG 59.137 41.667 0.00 0.00 0.00 2.32
3660 4147 4.860907 GCGACTACTTACGGAGAAAAATGA 59.139 41.667 0.00 0.00 0.00 2.57
3661 4148 5.346822 GCGACTACTTACGGAGAAAAATGAA 59.653 40.000 0.00 0.00 0.00 2.57
3662 4149 6.035758 GCGACTACTTACGGAGAAAAATGAAT 59.964 38.462 0.00 0.00 0.00 2.57
3663 4150 7.391786 CGACTACTTACGGAGAAAAATGAATG 58.608 38.462 0.00 0.00 0.00 2.67
3664 4151 7.274904 CGACTACTTACGGAGAAAAATGAATGA 59.725 37.037 0.00 0.00 0.00 2.57
3665 4152 8.842358 ACTACTTACGGAGAAAAATGAATGAA 57.158 30.769 0.00 0.00 0.00 2.57
3666 4153 9.449719 ACTACTTACGGAGAAAAATGAATGAAT 57.550 29.630 0.00 0.00 0.00 2.57
3667 4154 9.922305 CTACTTACGGAGAAAAATGAATGAATC 57.078 33.333 0.00 0.00 0.00 2.52
3668 4155 8.567285 ACTTACGGAGAAAAATGAATGAATCT 57.433 30.769 0.00 0.00 0.00 2.40
3669 4156 9.667107 ACTTACGGAGAAAAATGAATGAATCTA 57.333 29.630 0.00 0.00 0.00 1.98
3673 4160 9.838339 ACGGAGAAAAATGAATGAATCTATACT 57.162 29.630 0.00 0.00 0.00 2.12
3789 4276 1.758280 ACCAGTATCGCAATTACCCGA 59.242 47.619 0.00 0.00 37.91 5.14
3836 4344 2.042104 CGGTAGCCGTCTATTAACCG 57.958 55.000 0.00 0.00 42.73 4.44
3853 4361 2.537143 ACCGACTAGATGACCTGGTTT 58.463 47.619 0.00 0.00 36.67 3.27
3854 4362 2.233922 ACCGACTAGATGACCTGGTTTG 59.766 50.000 0.00 0.00 36.67 2.93
3855 4363 2.496070 CCGACTAGATGACCTGGTTTGA 59.504 50.000 0.00 0.00 36.67 2.69
3856 4364 3.133003 CCGACTAGATGACCTGGTTTGAT 59.867 47.826 0.00 0.00 36.67 2.57
3857 4365 4.115516 CGACTAGATGACCTGGTTTGATG 58.884 47.826 0.00 0.00 36.67 3.07
3859 4367 5.091261 ACTAGATGACCTGGTTTGATGAC 57.909 43.478 0.00 0.00 32.13 3.06
3867 4375 0.539438 TGGTTTGATGACCAGGGCAC 60.539 55.000 0.00 0.00 44.53 5.01
3868 4376 3.894560 TGGTTTGATGACCAGGGCACC 62.895 57.143 0.00 0.00 44.53 5.01
4053 4561 7.432148 TTTAGCATAAGGAGTATCACAGGAA 57.568 36.000 0.00 0.00 36.25 3.36
4066 4574 6.886459 AGTATCACAGGAATGTTTACTTGCAT 59.114 34.615 0.00 0.00 0.00 3.96
4107 4615 4.729868 ACAACTAAAGAGGCATTGTCCTT 58.270 39.130 1.91 0.00 36.38 3.36
4108 4616 4.520492 ACAACTAAAGAGGCATTGTCCTTG 59.480 41.667 1.91 0.00 36.38 3.61
4111 4619 3.439857 AAAGAGGCATTGTCCTTGCTA 57.560 42.857 1.91 0.00 40.03 3.49
4132 4664 1.298014 GTCCCTGAGCCCTTCACAG 59.702 63.158 0.00 0.00 33.83 3.66
4185 4729 1.891150 GACCCTCAGTTACGAACCTCA 59.109 52.381 0.00 0.00 0.00 3.86
4370 4933 4.497340 GCGAAAGTGAATTGAGGACAACAA 60.497 41.667 0.00 0.00 38.90 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.446994 TTGGGGAGGACCACGTGT 60.447 61.111 15.65 2.26 43.75 4.49
8 9 1.685820 CCTTCTTGGGGAGGACCAC 59.314 63.158 0.00 0.00 41.03 4.16
102 103 2.261671 CGTCCTCGTGGGTGGAAG 59.738 66.667 3.23 0.00 37.56 3.46
200 201 0.737715 CTCTTCAGGCCTTTCGGTCG 60.738 60.000 0.00 0.00 40.84 4.79
256 257 4.025229 TCTCGTATTTGCTGTCAAACACAC 60.025 41.667 6.73 3.25 44.11 3.82
269 270 8.515473 TCGTCCATATAACATTCTCGTATTTG 57.485 34.615 0.00 0.00 0.00 2.32
288 289 6.493802 AGCCTCTAGTCATATATTTTCGTCCA 59.506 38.462 0.00 0.00 0.00 4.02
348 349 4.133078 GTGATAGCCAGCTCTTATGCTTT 58.867 43.478 0.00 0.00 41.98 3.51
381 382 0.108472 GCCATGAAAAGAAGGCCTGC 60.108 55.000 5.69 3.13 41.25 4.85
386 387 5.807011 CGAATTTTAGGCCATGAAAAGAAGG 59.193 40.000 5.01 0.00 0.00 3.46
406 408 2.812011 CCTCCGTGAAAGGAAAACGAAT 59.188 45.455 0.00 0.00 40.25 3.34
491 497 6.372659 CAGCCAAAATAGTGTGAATAGTGACT 59.627 38.462 0.00 0.00 0.00 3.41
693 709 0.666577 CTTCACCGACCGAAGTGACC 60.667 60.000 1.98 0.00 42.49 4.02
717 733 4.754667 GTCCGGGTCCGCTTGTCC 62.755 72.222 0.00 0.00 38.24 4.02
736 752 1.834263 AGCTTCTCGGCCTATTGTTCT 59.166 47.619 0.00 0.00 0.00 3.01
890 1171 3.429580 GGGGATTGTGGGGGAGGG 61.430 72.222 0.00 0.00 0.00 4.30
1286 1568 6.203723 CCTTAATTTTAGGCGAATCTCTCCTG 59.796 42.308 0.00 0.00 31.78 3.86
1531 1824 3.688185 CACCAAGATCAGACCATCTGTTG 59.312 47.826 5.77 3.81 44.58 3.33
1619 1912 3.154827 TCAATGTTCCCAAGGGAGAAC 57.845 47.619 8.06 5.51 46.06 3.01
1775 2163 7.149307 TCTCGAACACTCAATACAACACATAA 58.851 34.615 0.00 0.00 0.00 1.90
1911 2366 0.179020 TGACCACAGACAGCAAAGGG 60.179 55.000 0.00 0.00 0.00 3.95
1923 2378 1.133823 ACCAGCACAAGAATGACCACA 60.134 47.619 0.00 0.00 0.00 4.17
1948 2409 1.474855 GGGCCATGCACAAACAAGTTT 60.475 47.619 4.39 0.00 0.00 2.66
1986 2448 6.183361 TGTGTGCCTTATACATGCTTCTAGAT 60.183 38.462 0.00 0.00 0.00 1.98
2055 2517 6.603201 CCTTAAAGCATTATCTCCTCCAAACA 59.397 38.462 0.00 0.00 0.00 2.83
2161 2624 5.994250 TCTAACCCTCTGGATTCAAATCAG 58.006 41.667 5.19 1.73 37.15 2.90
2309 2782 3.628032 TGGCAATTGTGAACTTGTCGTAA 59.372 39.130 7.40 0.00 29.58 3.18
2310 2783 3.206964 TGGCAATTGTGAACTTGTCGTA 58.793 40.909 7.40 0.00 29.58 3.43
2315 2788 4.735662 CCAATTGGCAATTGTGAACTTG 57.264 40.909 37.13 23.19 45.28 3.16
2337 2810 1.202268 CGAGCCGGTAGTTAACTCCTG 60.202 57.143 12.39 5.64 0.00 3.86
2338 2811 1.101331 CGAGCCGGTAGTTAACTCCT 58.899 55.000 12.39 2.13 0.00 3.69
2343 2816 2.357009 GTCAGATCGAGCCGGTAGTTAA 59.643 50.000 1.90 0.00 0.00 2.01
2346 2819 0.107116 AGTCAGATCGAGCCGGTAGT 60.107 55.000 1.90 0.00 0.00 2.73
2349 2822 2.418910 CCAGTCAGATCGAGCCGGT 61.419 63.158 1.90 0.00 0.00 5.28
2405 2878 1.347050 CTCATGATAGTGGGCCAGAGG 59.653 57.143 6.40 0.00 0.00 3.69
2426 2899 0.402861 TCCCCCACTTCCCAAACTCT 60.403 55.000 0.00 0.00 0.00 3.24
2427 2900 0.038310 CTCCCCCACTTCCCAAACTC 59.962 60.000 0.00 0.00 0.00 3.01
2428 2901 0.701310 ACTCCCCCACTTCCCAAACT 60.701 55.000 0.00 0.00 0.00 2.66
2429 2902 1.069775 TACTCCCCCACTTCCCAAAC 58.930 55.000 0.00 0.00 0.00 2.93
2448 2921 4.902448 ACTTAGACTCAGGAGACCAACTTT 59.098 41.667 2.79 0.00 0.00 2.66
2467 2940 9.959749 CTGCACTAAAAATCCAACTTTAACTTA 57.040 29.630 0.00 0.00 0.00 2.24
2506 2979 3.553922 CCTCTCACACGCTCTTCTTTCTT 60.554 47.826 0.00 0.00 0.00 2.52
2520 2993 1.610673 GGAGACAGGCCCTCTCACA 60.611 63.158 23.38 0.00 36.61 3.58
2529 3002 1.120530 TAAATCTCCGGGAGACAGGC 58.879 55.000 28.27 0.00 46.42 4.85
2620 3106 7.201785 GCAGGCAGCAGGTTTAAGTTTATAATA 60.202 37.037 0.00 0.00 44.79 0.98
2750 3236 1.202348 TCAGCAGTCATAGGTCACACG 59.798 52.381 0.00 0.00 0.00 4.49
2770 3256 3.250040 GCAGGACAAACGTACTTGACATT 59.750 43.478 6.97 0.00 0.00 2.71
3037 3523 5.348724 ACAGTAGTCATATCACAAGCAAACG 59.651 40.000 0.00 0.00 0.00 3.60
3047 3533 7.339466 ACATACACTCACACAGTAGTCATATCA 59.661 37.037 0.00 0.00 32.21 2.15
3101 3587 6.486657 AGCAGAGTAAAAAGAAATGCTACACA 59.513 34.615 0.00 0.00 40.52 3.72
3125 3611 7.481642 ACAAAAGTATATACGTCTCCACAGAG 58.518 38.462 7.23 0.00 41.93 3.35
3177 3663 6.792326 AGATTCAGCACAATCATGTTACATG 58.208 36.000 18.35 18.35 37.82 3.21
3221 3707 3.007182 AGAAAATGGGGTTAACGAGACGA 59.993 43.478 0.00 0.00 0.00 4.20
3249 3736 5.715439 TCCTTGTCATCCCATTCTGTAAT 57.285 39.130 0.00 0.00 0.00 1.89
3394 3881 4.217510 CAGCTTTGATATGGATGGGGAAA 58.782 43.478 0.00 0.00 0.00 3.13
3422 3909 4.872691 CAGTGCCTGATCGAAGATAAAGTT 59.127 41.667 0.00 0.00 45.12 2.66
3453 3940 0.319900 TCGCAGGTTCAGAGAGCAAC 60.320 55.000 0.00 0.00 0.00 4.17
3593 4080 8.852671 AGAGATATATTTAGGAATGGAGGGAG 57.147 38.462 0.00 0.00 0.00 4.30
3595 4082 9.898152 GAAAGAGATATATTTAGGAATGGAGGG 57.102 37.037 0.00 0.00 0.00 4.30
3616 4103 5.047306 TCGCTTGTTGGAATCTCTAGAAAGA 60.047 40.000 0.00 0.00 0.00 2.52
3617 4104 5.062809 GTCGCTTGTTGGAATCTCTAGAAAG 59.937 44.000 0.00 0.00 0.00 2.62
3618 4105 4.929808 GTCGCTTGTTGGAATCTCTAGAAA 59.070 41.667 0.00 0.00 0.00 2.52
3619 4106 4.220821 AGTCGCTTGTTGGAATCTCTAGAA 59.779 41.667 0.00 0.00 0.00 2.10
3620 4107 3.764434 AGTCGCTTGTTGGAATCTCTAGA 59.236 43.478 0.00 0.00 0.00 2.43
3621 4108 4.116747 AGTCGCTTGTTGGAATCTCTAG 57.883 45.455 0.00 0.00 0.00 2.43
3622 4109 4.705507 AGTAGTCGCTTGTTGGAATCTCTA 59.294 41.667 0.00 0.00 0.00 2.43
3623 4110 3.511934 AGTAGTCGCTTGTTGGAATCTCT 59.488 43.478 0.00 0.00 0.00 3.10
3624 4111 3.851098 AGTAGTCGCTTGTTGGAATCTC 58.149 45.455 0.00 0.00 0.00 2.75
3625 4112 3.963428 AGTAGTCGCTTGTTGGAATCT 57.037 42.857 0.00 0.00 0.00 2.40
3626 4113 4.031426 CGTAAGTAGTCGCTTGTTGGAATC 59.969 45.833 0.00 0.00 0.00 2.52
3627 4114 3.924686 CGTAAGTAGTCGCTTGTTGGAAT 59.075 43.478 0.00 0.00 0.00 3.01
3628 4115 3.311106 CGTAAGTAGTCGCTTGTTGGAA 58.689 45.455 0.00 0.00 0.00 3.53
3629 4116 2.352030 CCGTAAGTAGTCGCTTGTTGGA 60.352 50.000 0.00 0.00 0.00 3.53
3630 4117 1.990563 CCGTAAGTAGTCGCTTGTTGG 59.009 52.381 0.00 0.00 0.00 3.77
3631 4118 2.915463 CTCCGTAAGTAGTCGCTTGTTG 59.085 50.000 0.00 0.00 0.00 3.33
3632 4119 2.816087 TCTCCGTAAGTAGTCGCTTGTT 59.184 45.455 0.00 0.00 0.00 2.83
3633 4120 2.430465 TCTCCGTAAGTAGTCGCTTGT 58.570 47.619 0.00 0.00 0.00 3.16
3634 4121 3.482722 TTCTCCGTAAGTAGTCGCTTG 57.517 47.619 0.00 0.00 0.00 4.01
3635 4122 4.510038 TTTTCTCCGTAAGTAGTCGCTT 57.490 40.909 0.00 0.00 0.00 4.68
3636 4123 4.510038 TTTTTCTCCGTAAGTAGTCGCT 57.490 40.909 0.00 0.00 0.00 4.93
3637 4124 4.860907 TCATTTTTCTCCGTAAGTAGTCGC 59.139 41.667 0.00 0.00 0.00 5.19
3638 4125 6.939551 TTCATTTTTCTCCGTAAGTAGTCG 57.060 37.500 0.00 0.00 0.00 4.18
3639 4126 8.475331 TCATTCATTTTTCTCCGTAAGTAGTC 57.525 34.615 0.00 0.00 0.00 2.59
3640 4127 8.842358 TTCATTCATTTTTCTCCGTAAGTAGT 57.158 30.769 0.00 0.00 0.00 2.73
3641 4128 9.922305 GATTCATTCATTTTTCTCCGTAAGTAG 57.078 33.333 0.00 0.00 0.00 2.57
3642 4129 9.667107 AGATTCATTCATTTTTCTCCGTAAGTA 57.333 29.630 0.00 0.00 0.00 2.24
3643 4130 8.567285 AGATTCATTCATTTTTCTCCGTAAGT 57.433 30.769 0.00 0.00 0.00 2.24
3647 4134 9.838339 AGTATAGATTCATTCATTTTTCTCCGT 57.162 29.630 0.00 0.00 0.00 4.69
3745 4232 9.476202 GGTGCTCTGTTTCTAAATATTTGTTTT 57.524 29.630 11.05 0.00 0.00 2.43
3746 4233 8.637986 TGGTGCTCTGTTTCTAAATATTTGTTT 58.362 29.630 11.05 0.00 0.00 2.83
3747 4234 8.177119 TGGTGCTCTGTTTCTAAATATTTGTT 57.823 30.769 11.05 0.00 0.00 2.83
3748 4235 7.448469 ACTGGTGCTCTGTTTCTAAATATTTGT 59.552 33.333 11.05 0.00 0.00 2.83
3749 4236 7.820648 ACTGGTGCTCTGTTTCTAAATATTTG 58.179 34.615 11.05 1.65 0.00 2.32
3750 4237 9.686683 ATACTGGTGCTCTGTTTCTAAATATTT 57.313 29.630 5.89 5.89 0.00 1.40
3751 4238 9.331282 GATACTGGTGCTCTGTTTCTAAATATT 57.669 33.333 0.00 0.00 0.00 1.28
3752 4239 7.653713 CGATACTGGTGCTCTGTTTCTAAATAT 59.346 37.037 0.00 0.00 0.00 1.28
3753 4240 6.978659 CGATACTGGTGCTCTGTTTCTAAATA 59.021 38.462 0.00 0.00 0.00 1.40
3754 4241 5.812642 CGATACTGGTGCTCTGTTTCTAAAT 59.187 40.000 0.00 0.00 0.00 1.40
3755 4242 5.168569 CGATACTGGTGCTCTGTTTCTAAA 58.831 41.667 0.00 0.00 0.00 1.85
3756 4243 4.744570 CGATACTGGTGCTCTGTTTCTAA 58.255 43.478 0.00 0.00 0.00 2.10
3757 4244 3.428999 GCGATACTGGTGCTCTGTTTCTA 60.429 47.826 0.00 0.00 0.00 2.10
3758 4245 2.675317 GCGATACTGGTGCTCTGTTTCT 60.675 50.000 0.00 0.00 0.00 2.52
3759 4246 1.661112 GCGATACTGGTGCTCTGTTTC 59.339 52.381 0.00 0.00 0.00 2.78
3760 4247 1.001974 TGCGATACTGGTGCTCTGTTT 59.998 47.619 0.00 0.00 0.00 2.83
3761 4248 0.608130 TGCGATACTGGTGCTCTGTT 59.392 50.000 0.00 0.00 0.00 3.16
3762 4249 0.608130 TTGCGATACTGGTGCTCTGT 59.392 50.000 0.00 0.00 0.00 3.41
3763 4250 1.945387 ATTGCGATACTGGTGCTCTG 58.055 50.000 0.00 0.00 0.00 3.35
3764 4251 2.698855 AATTGCGATACTGGTGCTCT 57.301 45.000 0.00 0.00 0.00 4.09
3765 4252 2.544267 GGTAATTGCGATACTGGTGCTC 59.456 50.000 0.00 0.00 0.00 4.26
3766 4253 2.561569 GGTAATTGCGATACTGGTGCT 58.438 47.619 0.00 0.00 0.00 4.40
3767 4254 1.602377 GGGTAATTGCGATACTGGTGC 59.398 52.381 0.00 0.00 0.00 5.01
3768 4255 1.864711 CGGGTAATTGCGATACTGGTG 59.135 52.381 0.00 0.00 0.00 4.17
3769 4256 1.758280 TCGGGTAATTGCGATACTGGT 59.242 47.619 0.00 0.00 0.00 4.00
3770 4257 2.519377 TCGGGTAATTGCGATACTGG 57.481 50.000 0.00 0.00 0.00 4.00
3789 4276 0.252197 GGACCAGACCATACGGCTTT 59.748 55.000 0.00 0.00 34.57 3.51
3832 4340 2.233305 ACCAGGTCATCTAGTCGGTT 57.767 50.000 0.00 0.00 0.00 4.44
3834 4342 2.496070 TCAAACCAGGTCATCTAGTCGG 59.504 50.000 0.00 0.00 0.00 4.79
3836 4344 5.112686 GTCATCAAACCAGGTCATCTAGTC 58.887 45.833 0.00 0.00 0.00 2.59
3853 4361 2.204136 AGGGTGCCCTGGTCATCA 60.204 61.111 9.33 0.00 46.22 3.07
3863 4371 2.914059 TCTAATTCGCTTAAGGGTGCC 58.086 47.619 18.05 0.00 0.00 5.01
3867 4375 7.321745 ACATTCTTTCTAATTCGCTTAAGGG 57.678 36.000 13.14 13.14 0.00 3.95
3868 4376 9.922305 CTAACATTCTTTCTAATTCGCTTAAGG 57.078 33.333 4.29 0.00 0.00 2.69
4053 4561 8.432013 TGATACTCCTGATATGCAAGTAAACAT 58.568 33.333 0.00 0.00 0.00 2.71
4107 4615 1.990060 GGGCTCAGGGACAGTAGCA 60.990 63.158 0.00 0.00 36.68 3.49
4108 4616 1.268283 AAGGGCTCAGGGACAGTAGC 61.268 60.000 0.00 0.00 0.00 3.58
4111 4619 1.152030 TGAAGGGCTCAGGGACAGT 60.152 57.895 0.00 0.00 0.00 3.55
4132 4664 1.021920 GCGAGGCTTGAAACTCTCCC 61.022 60.000 5.76 0.00 0.00 4.30
4141 4673 1.512926 GAAGAAGTTGCGAGGCTTGA 58.487 50.000 5.76 0.00 0.00 3.02
4335 4884 4.921470 TCACTTTCGCTACAAGCATTAC 57.079 40.909 0.00 0.00 42.58 1.89


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.